ClinVar Genomic variation as it relates to human health
NM_000311.5(PRNP):c.305C>T (p.Pro102Leu)
The aggregate germline classification for this variant, typically for a monogenic or Mendelian disorder as in the ACMG/AMP guidelines, or for response to a drug. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the aggregate classification.
Stars represent the aggregate review status, or the level of review supporting the aggregate germline classification for this VCV record. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status. The number of submissions which contribute to this review status is shown in parentheses.
No data submitted for somatic clinical impact
No data submitted for oncogenicity
Variant Details
- Identifiers
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NM_000311.5(PRNP):c.305C>T (p.Pro102Leu)
Variation ID: 13395 Accession: VCV000013395.19
- Type and length
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single nucleotide variant, 1 bp
- Location
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Cytogenetic: 20p13 20: 4699525 (GRCh38) [ NCBI UCSC ] 20: 4680171 (GRCh37) [ NCBI UCSC ]
- Timeline in ClinVar
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First in ClinVar Help The date this variant first appeared in ClinVar with each type of classification.
Last submission Help The date of the most recent submission for each type of classification for this variant.
Last evaluated Help The most recent date that a submitter evaluated this variant for each type of classification.
Germline Apr 4, 2013 Feb 14, 2024 Jul 19, 2023 - HGVS
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Nucleotide Protein Molecular
consequenceNM_000311.5:c.305C>T MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_000302.1:p.Pro102Leu missense NM_000311.4:c.305C>T NM_001080121.3:c.305C>T NP_001073590.1:p.Pro102Leu missense NM_001080122.3:c.305C>T NP_001073591.1:p.Pro102Leu missense NM_001080123.3:c.305C>T NP_001073592.1:p.Pro102Leu missense NM_001271561.3:c.216C>T NP_001258490.1:p.Ala72= synonymous NM_183079.4:c.305C>T NP_898902.1:p.Pro102Leu missense NC_000020.11:g.4699525C>T NC_000020.10:g.4680171C>T NG_009087.1:g.18375C>T P04156:p.Pro102Leu - Protein change
- P102L
- Other names
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- Canonical SPDI
- NC_000020.11:4699524:C:T
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Functional
consequence HelpThe effect of the variant on RNA or protein function, based on experimental evidence from submitters.
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Global minor allele
frequency (GMAF) HelpThe global minor allele frequency calculated by the 1000 Genomes Project. The minor allele at this location is indicated in parentheses and may be different from the allele represented by this VCV record.
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Allele frequency
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The frequency of the allele represented by this VCV record.
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- Links
Genes
Gene | OMIM | ClinGen Gene Dosage Sensitivity Curation |
Variation Viewer
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Links to Variation Viewer, a genome browser to view variation data from NCBI databases. |
Related variants | ||
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HI score
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The haploinsufficiency score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team. |
TS score
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The triplosensitivity score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team. |
Within gene
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The number of variants in ClinVar that are contained within this gene, with a link to view the list of variants. |
All
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The number of variants in ClinVar for this gene, including smaller variants within the gene and larger CNVs that overlap or fully contain the gene. |
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PRNP | - | - |
GRCh38 GRCh37 |
174 | 209 |
Conditions - Germline
Condition
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The condition for this variant-condition (RCV) record in ClinVar. |
Classification
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The aggregate germline classification for this variant-condition (RCV) record in ClinVar. The number of submissions that contribute to this aggregate classification is shown in parentheses. (# of submissions) |
Review status
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The aggregate review status for this variant-condition (RCV) record in ClinVar. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status. |
Last evaluated
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The most recent date that a submitter evaluated this variant for the condition. |
Variation/condition record
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The RCV accession number, with most recent version number, for the variant-condition record, with a link to the RCV web page. |
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Pathogenic (2) |
no assertion criteria provided
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Jul 5, 2002 | RCV000014329.33 | |
Pathogenic (1) |
criteria provided, single submitter
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Jul 19, 2023 | RCV001203438.8 | |
Pathogenic (2) |
criteria provided, multiple submitters, no conflicts
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Feb 26, 2021 | RCV001269667.6 | |
Pathogenic (2) |
criteria provided, multiple submitters, no conflicts
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May 4, 2022 | RCV001813741.4 | |
Pathogenic (1) |
criteria provided, single submitter
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Jan 4, 2021 | RCV001642224.2 |
Submissions - Germline
Classification
Help
The submitted germline classification for each SCV record. (Last evaluated) |
Review status
Help
Stars represent the review status, or the level of review supporting the submitted (SCV) record. This value is calculated by NCBI based on data from the submitter. Read our rules for calculating the review status. This column also includes a link to the submitter’s assertion criteria if provided, and the collection method. (Assertion criteria) |
Condition
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The condition for the classification, provided by the submitter for this submitted (SCV) record. This column also includes the affected status and allele origin of individuals observed with this variant. |
Submitter
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The submitting organization for this submitted (SCV) record. This column also includes the SCV accession and version number, the date this SCV first appeared in ClinVar, and the date that this SCV was last updated in ClinVar. |
More information
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This column includes more information supporting the classification, including citations, the comment on classification, and detailed evidence provided as observations of the variant by the submitter. |
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Pathogenic
(Jul 19, 2023)
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criteria provided, single submitter
Method: clinical testing
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Huntington disease-like 1
Affected status: unknown
Allele origin:
germline
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Labcorp Genetics (formerly Invitae), Labcorp
Accession: SCV001374604.5
First in ClinVar: Jul 16, 2020 Last updated: Feb 14, 2024 |
Comment:
For these reasons, this variant has been classified as Pathogenic. Experimental studies have shown that this missense change affects PRNP function (PMID: 8698234). Advanced modeling … (more)
For these reasons, this variant has been classified as Pathogenic. Experimental studies have shown that this missense change affects PRNP function (PMID: 8698234). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is not expected to disrupt PRNP protein function. ClinVar contains an entry for this variant (Variation ID: 13395). This missense change has been observed in individual(s) with Gerstmann-Sträussler-Scheinker (GSS) syndrome (PMID: 2564168, 19696976, 22097954). In at least one individual the variant was observed to be de novo. It has also been observed to segregate with disease in related individuals. This variant is not present in population databases (gnomAD no frequency). This sequence change replaces proline, which is neutral and non-polar, with leucine, which is neutral and non-polar, at codon 102 of the PRNP protein (p.Pro102Leu). (less)
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Pathogenic
(Oct 12, 2015)
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criteria provided, single submitter
Method: clinical testing
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not provided
Affected status: yes
Allele origin:
germline
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Clinical Genetics and Genomics, Karolinska University Hospital
Accession: SCV001449821.1
First in ClinVar: Dec 11, 2020 Last updated: Dec 11, 2020 |
Number of individuals with the variant: 1
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Pathogenic
(Jan 04, 2021)
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criteria provided, single submitter
Method: research
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Spongiform encephalopathy with neuropsychiatric features
Affected status: yes
Allele origin:
unknown
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Molecular Medicine for Neurodegenerative and Neuromuscular Diseases Unit, IRCCS Fondazione Stella Maris
Accession: SCV001519189.1
First in ClinVar: Sep 19, 2021 Last updated: Sep 19, 2021 |
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Pathogenic
(Jan 05, 2022)
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criteria provided, single submitter
Method: clinical testing
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Inherited Creutzfeldt-Jakob disease
Affected status: yes
Allele origin:
germline
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DASA
Accession: SCV002061168.1
First in ClinVar: Jan 22, 2022 Last updated: Jan 22, 2022 |
Comment:
The c.305C>T;p.(Pro102Leu) missense variant has been observed in affected individual(s) and ClinVar contains an entry for this variant (ClinVar ID: 13395; OMIM: 176640.0002; PMID: 1672296; … (more)
The c.305C>T;p.(Pro102Leu) missense variant has been observed in affected individual(s) and ClinVar contains an entry for this variant (ClinVar ID: 13395; OMIM: 176640.0002; PMID: 1672296; 2564168; 2572450; 2564168; 19696976; 22097954) - PS4.This variant is not present in population databases (rs74315401, gnomAD; ABraOM no frequency - http://abraom.ib.usp.br/) - PM2. The variant was assumed de novo, but without confirmation of paternity and maternity (PMID: 22097954) - PM6. The variant co-segregated with disease in multiple affected family members (PMID: 1672296; 2564168; 2572450) - PP1_strong. Multiple lines of computational evidence support a deleterious effect on the gene or gene product - PP3. In summary, the currently available evidence indicates that the variant is pathogenic. (less)
Number of individuals with the variant: 1
Sex: male
Geographic origin: Brazil
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Pathogenic
(Feb 26, 2021)
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criteria provided, single submitter
Method: clinical testing
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not provided
Affected status: yes
Allele origin:
germline
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Genetic Services Laboratory, University of Chicago
Accession: SCV002064352.1
First in ClinVar: Jan 29, 2022 Last updated: Jan 29, 2022 |
Comment:
DNA sequence analysis of the PRNP gene demonstrated a sequence change, c.305C>T, in exon 2 that results in an amino acid change, p.Pro102Leu. This sequence … (more)
DNA sequence analysis of the PRNP gene demonstrated a sequence change, c.305C>T, in exon 2 that results in an amino acid change, p.Pro102Leu. This sequence change is absent from the gnomAD general population database. This sequence change has been previously described in individuals and families with Gerstmann-Straussler disease (PMIDs: 2564168, 2572450, 2783132, 19696976). The p.Pro102Leu change affects a highly conserved amino acid residue of the PRNP protein. The p.Pro102Leu variant appears to be deleterious using several in-silico pathogenicity prediction tools (SIFT, PolyPhen2, REVEL). Functional studies demonstrate cell lines with p.Pro102Leu result in decreased expression of normal prion protein and accumulation of abnormal prion protein on the cell surface (PMID: 11967261). Transgenic mice with p.Pro102Leu develop neurodegeneration (PMID: 8698234). These collective evidences indicate that this sequence change is pathogenic. (less)
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Pathogenic
(May 04, 2022)
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criteria provided, single submitter
Method: clinical testing
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Inherited Creutzfeldt-Jakob disease
Affected status: unknown
Allele origin:
germline
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Mendelics
Accession: SCV002518906.1
First in ClinVar: May 21, 2022 Last updated: May 21, 2022 |
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Pathogenic
(Jul 05, 2002)
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no assertion criteria provided
Method: literature only
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GERSTMANN-STRAUSSLER DISEASE
Affected status: not provided
Allele origin:
germline
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OMIM
Accession: SCV000034578.9
First in ClinVar: Apr 04, 2013 Last updated: Sep 03, 2018 |
Comment on evidence:
In affected members of 2 unrelated families with autosomal dominant inheritance of Gerstmann-Straussler disease (GSD; 137440), Hsiao et al. (1989) identified a C-to-T transition in … (more)
In affected members of 2 unrelated families with autosomal dominant inheritance of Gerstmann-Straussler disease (GSD; 137440), Hsiao et al. (1989) identified a C-to-T transition in the PRNP gene, resulting in a pro102-to-leu (P102L) substitution. The mutation was not identified in 100 Caucasian control individuals. The authors reported that the families presented with ataxia. One of the families also had a polymorphism resulting from a 'silent' A-to-G substitution at the third position of alanine codon 117. Goldgaber et al. (1989) identified the P102L mutation in 3 affected members of a family with GSD. The base substitution responsible for the change in codon 102 may have involved deamination of a methylated cytosine situated 5-prime to guanine, a CpG mutation. The proline at codon 102 seems to be highly conserved, as all rodent proline genes sequenced to date also encode a proline at the equivalent codon. Doh-ura et al. (1989) reported that the P102L mutation was identified in all 11 Japanese GSD patients studied. Speer et al. (1991) found linkage to the P102L mutation in a large German family with GSD. Three asymptomatic members of the German family carried the substitution; their ages, 41, 42, and 42, were below the mean for age of onset (47 years) for GSD in this family. In a 36-year-old woman with GSD who belonged to the original family reported by Gerstmann et al. (1936) and Seitelberger (1962), Kretzschmar et al. (1991) identified a heterozygous P102L mutation in the PRNP gene. Goldfarb et al. (1990) excluded the P102L mutation in patients with CJD and kuru, suggesting that it is specific for GSD. Goldhammer et al. (1993) described an Ashkenazi Jewish family living in Israel in which Gerstmann-Straussler syndrome was due to the P102L mutation in the PRNP gene. Doh-ura et al. (1990) demonstrated the P102L mutation in 6 of 7 patients with Creutzfeldt-Jakob disease with congophilic kuru plaques. No patient with CJD without congophilic kuru plaques had this allele. They also found the leu102 allele in some unaffected relatives of 3 patients, although there was no known familial occurrence of a similar neurologic disorder. Doh-ura et al. (1990) concluded that CJD with congophilic kuru plaques should be categorized as Gerstmann-Straussler syndrome, not CJD. Parchi et al. (1998) reported 7 unrelated patients with GSS who carried a heterozygous P102L mutation. Two major types of PrP(res) were identified: an unglycosylated 8-kD fragment, found in all patients, and an additional unglycosylated 21-kD fragment, found in 5 of the 7 patients. Additional 27- and 29-kD fragments that were glycosylated forms of the 21-kD fragment were also found in the 5 patients with the 21-kD fragment. The 8-kD fragment was ragged at both the N- and C-terminal ends, whereas the 21-kD fragment was truncated only at the N-terminal end. The 8-kD fragment correlated with the presence of amyloid plaques, whereas the 21-kD fragment correlated with spongiform degeneration. These PrP(res) fragments were present in vivo. The findings suggested that the neuropathology of prion diseases largely depends on the type of PrP(res) fragment. In neuroblastoma cells transfected with the P102L mutation, Mishra et al. (2002) showed that the processing and turnover of the prion protein was altered, resulting in decreased expression of a normal 18-kD fragment and increased accumulation of a 20-kD fragment on the surface of these cells. The authors suggested that this alteration may render the cells more susceptible to pathogenic prion protein infection and toxicity via amyloidogenesis or amplification of a neurotoxic signal initiated by a pathogenic prion protein. (less)
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not provided
(-)
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no classification provided
Method: literature only
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Gerstmann-Straussler-Scheinker syndrome
Affected status: unknown
Allele origin:
germline
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GeneReviews
Accession: SCV000040593.3
First in ClinVar: Apr 04, 2013 Last updated: Oct 01, 2022 |
Comment:
Associated with Gerstmann-Straussler-Scheinker syndrome phenotype. One of the five most common variants that account for 85% of genetic prion disease.
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Germline Functional Evidence
There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar. |
Citations for germline classification of this variant
HelpTitle | Author | Journal | Year | Link |
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Genetic Prion Disease. | Adam MP | - | 2021 | PMID: 20301407 |
Genetic Creutzfeldt-Jakob disease. | Ladogana A | Handbook of clinical neurology | 2018 | PMID: 29887139 |
Spectrum and frequency of GJB2 mutations in a cohort of 264 Portuguese nonsyndromic sensorineural hearing loss patients. | Matos TD | International journal of audiology | 2013 | PMID: 23668481 |
De novo P102L mutation in a patient with Gerstmann-Sträussler-Scheinker disease. | Kojović M | European journal of neurology | 2011 | PMID: 22097954 |
Transmissible spongiform encephalopathies with P102L mutation of PRNP manifesting different phenotypes: clinical, neuroimaging, and electrophysiological studies in Chinese kindred in Taiwan. | Chi NF | Journal of neurology | 2010 | PMID: 19696976 |
A multicenter study of the frequency and distribution of GJB2 and GJB6 mutations in a large North American cohort. | Putcha GV | Genetics in medicine : official journal of the American College of Medical Genetics | 2007 | PMID: 17666888 |
GJB2 mutations and degree of hearing loss: a multicenter study. | Snoeckx RL | American journal of human genetics | 2005 | PMID: 16380907 |
GJB2 and GJB6 mutations: genotypic and phenotypic correlations in a large cohort of hearing-impaired patients. | Marlin S | Archives of otolaryngology--head & neck surgery | 2005 | PMID: 15967879 |
Effectiveness of sequencing connexin 26 (GJB2) in cases of familial or sporadic childhood deafness referred for molecular diagnostic testing. | Wu BL | Genetics in medicine : official journal of the American College of Medical Genetics | 2002 | PMID: 12172394 |
Cell surface accumulation of a truncated transmembrane prion protein in Gerstmann-Straussler-Scheinker disease P102L. | Mishra RS | The Journal of biological chemistry | 2002 | PMID: 11967261 |
Different patterns of truncated prion protein fragments correlate with distinct phenotypes in P102L Gerstmann-Sträussler-Scheinker disease. | Parchi P | Proceedings of the National Academy of Sciences of the United States of America | 1998 | PMID: 9653185 |
Interactions between wild-type and mutant prion proteins modulate neurodegeneration in transgenic mice. | Telling GC | Genes & development | 1996 | PMID: 8698234 |
An Israeli family with Gerstmann-Sträussler-Scheinker disease manifesting the codon 102 mutation in the prion protein gene. | Goldhammer Y | Neurology | 1993 | PMID: 7902971 |
Prion protein mutation in family first reported by Gerstmann, Sträussler, and Scheinker. | Kretzschmar HA | Lancet (London, England) | 1991 | PMID: 1674033 |
Support of linkage of Gerstmann-Sträussler-Scheinker syndrome to the prion protein gene on chromosome 20p12-pter. | Speer MC | Genomics | 1991 | PMID: 1672296 |
Creutzfeldt-Jakob disease and kuru patients lack a mutation consistently found in the Gerstmann-Sträussler-Scheinker syndrome. | Goldfarb LG | Experimental neurology | 1990 | PMID: 2190844 |
Creutzfeldt-Jakob disease patients with congophilic kuru plaques have the missense variant prion protein common to Gerstmann-Sträussler syndrome. | Doh-ura K | Annals of neurology | 1990 | PMID: 2180366 |
Pro----leu change at position 102 of prion protein is the most common but not the sole mutation related to Gerstmann-Sträussler syndrome. | Doh-ura K | Biochemical and biophysical research communications | 1989 | PMID: 2783132 |
Mutations in familial Creutzfeldt-Jakob disease and Gerstmann-Sträussler-Scheinker's syndrome. | Goldgaber D | Experimental neurology | 1989 | PMID: 2572450 |
Linkage of a prion protein missense variant to Gerstmann-Sträussler syndrome. | Hsiao K | Nature | 1989 | PMID: 2564168 |
[An unusual hereditary familial disease of the central nervous system]. | VON BRAUNMUHL A | Archiv fur Psychiatrie und Nervenkrankheiten, vereinigt mit Zeitschrift fur die gesamte Neurologie und Psychiatrie | 1954 | PMID: 13171903 |
Seitelberger, F. Eigenartige familiaer-hereditaere Krankheit des Zentralnervensystems in einer Niederoesterreichischen Sippe (zugleich ein Beitrag zur vergleichenden Neuropathologie des Kuru). Wien. Klin. Wschr. 74: 687-691, 1962. | - | - | - | - |
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Text-mined citations for rs74315401 ...
HelpRecord last updated Sep 29, 2024
This date represents the last time this VCV record was updated. The update may be due to an update to one of the included submitted records (SCVs), or due to an update that ClinVar made to the variant such as adding HGVS expressions or a rs number. So this date may be different from the date of the “most recent submission” reported at the top of this page.